Malaria is the most common cause of morbidity and mortality in children under 5 in Mali. Health centres provide primary care, including malaria treatment, under a system of cost recovery. In 2005, Médecins sans Frontieres (MSF) started supporting health centres in Kangaba with the provision of rapid malaria diagnostic tests and artemisinin-based combination therapy. Initially MSF subsidized malaria tests and drugs to reduce the overall cost for patients. In a second phase, MSF abolished fees for all children under 5 irrespective of their illness and for pregnant women with fever. This second phase was associated with a trebling of both primary health care utilization and malaria treatment coverage for these groups. MSF's experience in Mali suggests that removing user fees for vulnerable groups significantly improves utilization and coverage of essential health services, including for malaria interventions. This effect is far more marked than simply subsidizing or providing malaria drugs and diagnostic tests free of charge. Following the free care strategy, utilization of services increased significantly and under-5 mortality was reduced. Fee removal also allowed for more efficient use of existing resources, reducing average cost per patient treated. These results are particularly relevant for the context of Mali and other countries with ambitious malaria treatment coverage objectives, in accordance with the United Nations Millennium Development Goals. This article questions the effectiveness of the current national policy, and the effectiveness of reducing the cost of drugs only (i.e. partial subsidies) or providing malaria tests and drugs free for under-5s, without abolishing other related fees. National and international budgets, in particular those that target health systems strengthening, could be used to complement existing subsidies and be directed towards effective abolition of user fees. This would contribute to increasing the impact of interventions on population health and, in turn, the effectiveness of aid.